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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2023-05-18, 16:50 CEST based on data in:

        General Statistics

        Showing 414/414 rows and 4/6 columns.
        Sample Name% Dups% GCMedian Read LengthM Seqs
        SAMEA1964687_qc_fHP_1
        11.5%
        46%
        89 bp
        28.2
        SAMEA1964687_qc_fHP_2
        11.4%
        46%
        89 bp
        28.2
        SAMEA1964695_qc_fHP_1
        12.7%
        39%
        72 bp
        16.6
        SAMEA1964695_qc_fHP_2
        12.6%
        39%
        74 bp
        16.6
        SAMEA1964852_qc_fHP_1
        10.1%
        40%
        74 bp
        17.3
        SAMEA1964852_qc_fHP_2
        8.8%
        39%
        74 bp
        17.3
        SAMEA1965149_qc_fHP_1
        8.2%
        45%
        89 bp
        37.2
        SAMEA1965149_qc_fHP_2
        8.1%
        45%
        89 bp
        37.2
        SAMEA1965858_qc_fHP_1
        20.6%
        44%
        89 bp
        46.0
        SAMEA1965858_qc_fHP_2
        20.1%
        44%
        89 bp
        46.0
        SAMEA1966821_qc_fHP_1
        7.0%
        39%
        72 bp
        14.9
        SAMEA1966821_qc_fHP_2
        7.0%
        39%
        74 bp
        14.9
        SAMEA1967319_qc_fHP_1
        34.1%
        44%
        89 bp
        31.7
        SAMEA1967319_qc_fHP_2
        33.1%
        44%
        89 bp
        31.7
        SAMEA1967891_qc_fHP_1
        15.8%
        42%
        74 bp
        16.3
        SAMEA1967891_qc_fHP_2
        15.4%
        42%
        74 bp
        16.3
        SAMEA1969126_qc_fHP_1
        9.8%
        43%
        72 bp
        17.5
        SAMEA1969126_qc_fHP_2
        9.5%
        43%
        74 bp
        17.5
        SAMEA1969178_qc_fHP_1
        8.3%
        39%
        74 bp
        14.9
        SAMEA1969178_qc_fHP_2
        8.2%
        38%
        74 bp
        14.9
        SAMEA1969417_qc_fHP_1
        27.9%
        45%
        89 bp
        26.8
        SAMEA1969417_qc_fHP_2
        27.6%
        45%
        89 bp
        26.8
        SAMEA1970858_qc_fHP_1
        13.2%
        48%
        89 bp
        35.7
        SAMEA1970858_qc_fHP_2
        13.1%
        48%
        89 bp
        35.7
        SAMEA1971210_qc_fHP_1
        21.2%
        45%
        89 bp
        36.3
        SAMEA1971210_qc_fHP_2
        20.2%
        46%
        89 bp
        36.3
        SAMEA1972188_qc_fHP_1
        28.9%
        44%
        89 bp
        43.5
        SAMEA1972188_qc_fHP_2
        28.4%
        44%
        89 bp
        43.5
        SAMEA1972381_qc_fHP_1
        9.9%
        45%
        89 bp
        34.7
        SAMEA1972381_qc_fHP_2
        9.6%
        46%
        89 bp
        34.7
        SAMEA2142349_qc_fHP_1
        10.0%
        46%
        89 bp
        40.1
        SAMEA2142349_qc_fHP_2
        9.7%
        46%
        89 bp
        40.1
        SAMEA2142525_qc_fHP_1
        23.6%
        41%
        74 bp
        29.3
        SAMEA2142525_qc_fHP_2
        23.6%
        41%
        74 bp
        29.3
        SAMEA2142594_qc_fHP_1
        5.8%
        37%
        74 bp
        16.4
        SAMEA2142594_qc_fHP_2
        5.6%
        37%
        74 bp
        16.4
        SAMEA2142793_qc_fHP_1
        18.4%
        42%
        74 bp
        28.1
        SAMEA2142793_qc_fHP_2
        18.4%
        42%
        74 bp
        28.1
        SAMEA2142846_qc_fHP_1
        6.6%
        41%
        72 bp
        15.9
        SAMEA2142846_qc_fHP_2
        5.9%
        41%
        74 bp
        15.9
        SAMEA2142848_qc_fHP_1
        10.8%
        42%
        72 bp
        17.4
        SAMEA2142848_qc_fHP_2
        10.5%
        42%
        74 bp
        17.4
        SAMEA2142970_qc_fHP_1
        9.8%
        45%
        89 bp
        36.8
        SAMEA2142970_qc_fHP_2
        9.4%
        45%
        89 bp
        36.8
        SAMEA2143074_qc_fHP_1
        19.9%
        44%
        89 bp
        40.7
        SAMEA2143074_qc_fHP_2
        19.6%
        44%
        89 bp
        40.7
        SAMEA2143633_qc_fHP_1
        12.4%
        47%
        89 bp
        38.7
        SAMEA2143633_qc_fHP_2
        11.7%
        47%
        89 bp
        38.7
        SAMEA2143863_qc_fHP_1
        11.5%
        46%
        89 bp
        31.8
        SAMEA2143863_qc_fHP_2
        11.0%
        46%
        89 bp
        31.8
        SAMEA2143980_qc_fHP_1
        6.7%
        42%
        74 bp
        10.8
        SAMEA2143980_qc_fHP_2
        6.1%
        42%
        74 bp
        10.8
        SAMEA2144223_qc_fHP_1
        24.8%
        46%
        89 bp
        38.8
        SAMEA2144223_qc_fHP_2
        24.0%
        46%
        89 bp
        38.8
        SAMEA2144304_qc_fHP_1
        11.6%
        46%
        89 bp
        34.7
        SAMEA2144304_qc_fHP_2
        11.1%
        46%
        89 bp
        34.7
        SAMEA2144396_qc_fHP_1
        6.4%
        46%
        89 bp
        29.4
        SAMEA2144396_qc_fHP_2
        6.2%
        46%
        89 bp
        29.4
        SAMEA2144525_qc_fHP_1
        12.6%
        40%
        72 bp
        17.3
        SAMEA2144525_qc_fHP_2
        12.2%
        40%
        74 bp
        17.3
        SAMEA2144555_qc_fHP_1
        11.7%
        46%
        89 bp
        38.5
        SAMEA2144555_qc_fHP_2
        11.2%
        47%
        89 bp
        38.5
        SAMEA2144578_qc_fHP_1
        20.5%
        41%
        72 bp
        18.5
        SAMEA2144578_qc_fHP_2
        20.2%
        41%
        74 bp
        18.5
        SAMEA2144588_qc_fHP_1
        11.6%
        40%
        72 bp
        20.4
        SAMEA2144588_qc_fHP_2
        11.6%
        40%
        74 bp
        20.4
        SAMEA2144623_qc_fHP_1
        12.1%
        42%
        74 bp
        28.1
        SAMEA2144623_qc_fHP_2
        12.3%
        42%
        74 bp
        28.1
        SAMEA2144980_qc_fHP_1
        22.9%
        46%
        89 bp
        35.4
        SAMEA2144980_qc_fHP_2
        22.5%
        46%
        89 bp
        35.4
        SAMEA2145068_qc_fHP_1
        13.8%
        38%
        72 bp
        16.1
        SAMEA2145068_qc_fHP_2
        13.7%
        38%
        74 bp
        16.1
        SAMEA2145301_qc_fHP_1
        13.3%
        41%
        74 bp
        28.7
        SAMEA2145301_qc_fHP_2
        13.0%
        41%
        74 bp
        28.7
        SAMEA2145365_qc_fHP_1
        8.7%
        45%
        89 bp
        40.0
        SAMEA2145365_qc_fHP_2
        8.3%
        45%
        89 bp
        40.0
        SAMEA2145582_qc_fHP_1
        8.6%
        41%
        74 bp
        14.2
        SAMEA2145582_qc_fHP_2
        8.0%
        41%
        74 bp
        14.2
        SAMEA2145648_qc_fHP_1
        15.1%
        40%
        74 bp
        13.1
        SAMEA2145648_qc_fHP_2
        13.3%
        39%
        74 bp
        13.1
        SAMEA2145758_qc_fHP_1
        13.1%
        40%
        68 bp
        17.8
        SAMEA2145758_qc_fHP_2
        12.9%
        40%
        74 bp
        17.8
        SAMEA2145815_qc_fHP_1
        8.1%
        45%
        89 bp
        33.1
        SAMEA2145815_qc_fHP_2
        7.9%
        45%
        89 bp
        33.1
        SAMEA2146009_qc_fHP_1
        15.2%
        46%
        89 bp
        37.7
        SAMEA2146009_qc_fHP_2
        14.6%
        46%
        89 bp
        37.7
        SAMEA2146107_qc_fHP_1
        7.6%
        48%
        89 bp
        27.5
        SAMEA2146107_qc_fHP_2
        7.3%
        48%
        89 bp
        27.5
        SAMEA2146320_qc_fHP_1
        7.0%
        40%
        72 bp
        18.5
        SAMEA2146320_qc_fHP_2
        6.7%
        40%
        74 bp
        18.5
        SAMEA2146477_qc_fHP_1
        8.7%
        45%
        89 bp
        35.7
        SAMEA2146477_qc_fHP_2
        8.4%
        45%
        89 bp
        35.7
        SAMEA2146552_qc_fHP_1
        16.1%
        46%
        89 bp
        45.1
        SAMEA2146552_qc_fHP_2
        15.4%
        47%
        89 bp
        45.1
        SAMEA2146600_qc_fHP_1
        15.8%
        44%
        89 bp
        32.1
        SAMEA2146600_qc_fHP_2
        15.5%
        44%
        89 bp
        32.1
        SAMEA2146682_qc_fHP_1
        4.3%
        38%
        72 bp
        16.9
        SAMEA2146682_qc_fHP_2
        4.2%
        38%
        74 bp
        16.9
        SAMEA2146731_qc_fHP_1
        10.4%
        40%
        72 bp
        19.3
        SAMEA2146731_qc_fHP_2
        10.2%
        39%
        74 bp
        19.3
        SAMEA2146908_qc_fHP_1
        9.9%
        40%
        72 bp
        16.7
        SAMEA2146908_qc_fHP_2
        9.8%
        40%
        74 bp
        16.7
        SAMEA2147022_qc_fHP_1
        18.7%
        40%
        72 bp
        19.5
        SAMEA2147022_qc_fHP_2
        18.2%
        40%
        74 bp
        19.5
        SAMEA2147036_qc_fHP_1
        22.2%
        45%
        89 bp
        36.5
        SAMEA2147036_qc_fHP_2
        21.5%
        45%
        89 bp
        36.5
        SAMEA2147070_qc_fHP_1
        8.9%
        41%
        72 bp
        18.6
        SAMEA2147070_qc_fHP_2
        8.7%
        41%
        74 bp
        18.6
        SAMEA2147092_qc_fHP_1
        17.9%
        38%
        74 bp
        12.9
        SAMEA2147092_qc_fHP_2
        14.8%
        37%
        74 bp
        12.9
        SAMEA2147114_qc_fHP_1
        11.0%
        41%
        74 bp
        26.9
        SAMEA2147114_qc_fHP_2
        10.8%
        41%
        74 bp
        26.9
        SAMEA2147216_qc_fHP_1
        16.5%
        41%
        72 bp
        17.8
        SAMEA2147216_qc_fHP_2
        16.3%
        41%
        74 bp
        17.8
        SAMEA2147326_qc_fHP_1
        22.0%
        43%
        89 bp
        36.3
        SAMEA2147326_qc_fHP_2
        21.5%
        43%
        89 bp
        36.3
        SAMEA2147384_qc_fHP_1
        17.4%
        40%
        72 bp
        19.7
        SAMEA2147384_qc_fHP_2
        16.9%
        40%
        74 bp
        19.7
        SAMEA2147587_qc_fHP_1
        12.7%
        41%
        74 bp
        27.6
        SAMEA2147587_qc_fHP_2
        11.8%
        41%
        74 bp
        27.6
        SAMEA2147589_qc_fHP_1
        22.1%
        41%
        72 bp
        20.3
        SAMEA2147589_qc_fHP_2
        21.8%
        41%
        74 bp
        20.3
        SAMEA2147991_qc_fHP_1
        18.1%
        41%
        74 bp
        25.7
        SAMEA2147991_qc_fHP_2
        18.0%
        41%
        74 bp
        25.7
        SAMEA2148094_qc_fHP_1
        16.2%
        46%
        89 bp
        41.9
        SAMEA2148094_qc_fHP_2
        15.9%
        46%
        89 bp
        41.9
        SAMEA2148105_qc_fHP_1
        37.4%
        42%
        72 bp
        20.0
        SAMEA2148105_qc_fHP_2
        37.6%
        41%
        74 bp
        20.0
        SAMEA2148265_qc_fHP_1
        13.7%
        41%
        74 bp
        15.3
        SAMEA2148265_qc_fHP_2
        12.8%
        41%
        74 bp
        15.3
        SAMEA2148412_qc_fHP_1
        9.6%
        44%
        89 bp
        36.2
        SAMEA2148412_qc_fHP_2
        9.3%
        44%
        89 bp
        36.2
        SAMEA2148549_qc_fHP_1
        9.2%
        40%
        74 bp
        11.7
        SAMEA2148549_qc_fHP_2
        5.7%
        39%
        74 bp
        11.7
        SAMEA2148755_qc_fHP_1
        12.4%
        45%
        89 bp
        37.7
        SAMEA2148755_qc_fHP_2
        12.2%
        45%
        89 bp
        37.7
        SAMEA2149068_qc_fHP_1
        22.9%
        44%
        89 bp
        42.2
        SAMEA2149068_qc_fHP_2
        22.5%
        44%
        89 bp
        42.2
        SAMEA2149228_qc_fHP_1
        14.9%
        45%
        89 bp
        33.3
        SAMEA2149228_qc_fHP_2
        14.1%
        45%
        89 bp
        33.3
        SAMEA2149241_qc_fHP_1
        18.2%
        45%
        89 bp
        40.8
        SAMEA2149241_qc_fHP_2
        17.8%
        45%
        89 bp
        40.8
        SAMEA2149271_qc_fHP_1
        17.6%
        45%
        89 bp
        27.6
        SAMEA2149271_qc_fHP_2
        17.6%
        45%
        89 bp
        27.6
        SAMEA2149539_qc_fHP_1
        11.4%
        40%
        72 bp
        21.7
        SAMEA2149539_qc_fHP_2
        10.8%
        39%
        74 bp
        21.7
        SAMEA2149636_qc_fHP_1
        15.3%
        44%
        89 bp
        42.1
        SAMEA2149636_qc_fHP_2
        14.9%
        44%
        89 bp
        42.1
        SAMEA2149794_qc_fHP_1
        32.0%
        46%
        89 bp
        38.6
        SAMEA2149794_qc_fHP_2
        31.1%
        46%
        89 bp
        38.6
        SAMEA2149983_qc_fHP_1
        13.2%
        46%
        89 bp
        37.1
        SAMEA2149983_qc_fHP_2
        13.0%
        46%
        89 bp
        37.1
        SAMEA2150168_qc_fHP_1
        20.5%
        44%
        89 bp
        44.6
        SAMEA2150168_qc_fHP_2
        20.6%
        44%
        89 bp
        44.6
        SAMEA2150234_qc_fHP_1
        18.3%
        46%
        89 bp
        36.9
        SAMEA2150234_qc_fHP_2
        17.8%
        46%
        89 bp
        36.9
        SAMEA2150447_qc_fHP_1
        5.8%
        41%
        74 bp
        12.6
        SAMEA2150447_qc_fHP_2
        5.2%
        40%
        74 bp
        12.6
        SAMEA2150563_qc_fHP_1
        10.3%
        45%
        89 bp
        25.2
        SAMEA2150563_qc_fHP_2
        10.2%
        45%
        89 bp
        25.2
        SAMEA2150726_qc_fHP_1
        8.0%
        46%
        89 bp
        36.5
        SAMEA2150726_qc_fHP_2
        7.8%
        46%
        89 bp
        36.5
        SAMEA2150876_qc_fHP_1
        15.4%
        43%
        72 bp
        20.1
        SAMEA2150876_qc_fHP_2
        15.3%
        42%
        74 bp
        20.1
        SAMEA2150909_qc_fHP_1
        10.2%
        40%
        72 bp
        15.1
        SAMEA2150909_qc_fHP_2
        10.1%
        40%
        74 bp
        15.1
        SAMEA2151007_qc_fHP_1
        8.3%
        45%
        89 bp
        33.3
        SAMEA2151007_qc_fHP_2
        8.2%
        45%
        89 bp
        33.3
        SAMEA2151010_qc_fHP_1
        15.9%
        45%
        89 bp
        39.8
        SAMEA2151010_qc_fHP_2
        15.6%
        45%
        89 bp
        39.8
        SAMEA2151034_qc_fHP_1
        15.5%
        43%
        74 bp
        27.6
        SAMEA2151034_qc_fHP_2
        15.3%
        43%
        74 bp
        27.6
        SAMEA2151383_qc_fHP_1
        14.9%
        48%
        89 bp
        34.8
        SAMEA2151383_qc_fHP_2
        14.3%
        48%
        89 bp
        34.8
        SAMEA2151391_qc_fHP_1
        11.4%
        38%
        72 bp
        20.2
        SAMEA2151391_qc_fHP_2
        11.0%
        38%
        74 bp
        20.2
        SAMEA2151439_qc_fHP_1
        16.1%
        47%
        89 bp
        29.5
        SAMEA2151439_qc_fHP_2
        15.8%
        47%
        89 bp
        29.5
        SAMEA2151606_qc_fHP_1
        6.5%
        41%
        68 bp
        14.8
        SAMEA2151606_qc_fHP_2
        6.4%
        41%
        74 bp
        14.8
        SAMEA2151633_qc_fHP_1
        25.1%
        46%
        89 bp
        27.7
        SAMEA2151633_qc_fHP_2
        24.3%
        46%
        89 bp
        27.7
        SAMEA2151677_qc_fHP_1
        4.5%
        41%
        72 bp
        13.9
        SAMEA2151677_qc_fHP_2
        4.3%
        41%
        74 bp
        13.9
        SAMEA2151703_qc_fHP_1
        17.7%
        45%
        89 bp
        36.9
        SAMEA2151703_qc_fHP_2
        17.3%
        45%
        89 bp
        36.9
        SAMEA2151838_qc_fHP_1
        13.8%
        45%
        74 bp
        24.1
        SAMEA2151838_qc_fHP_2
        13.7%
        45%
        74 bp
        24.1
        SAMEA2152063_qc_fHP_1
        24.1%
        45%
        89 bp
        33.9
        SAMEA2152063_qc_fHP_2
        23.6%
        45%
        89 bp
        33.9
        SAMEA2152064_qc_fHP_1
        9.0%
        48%
        89 bp
        41.9
        SAMEA2152064_qc_fHP_2
        8.9%
        49%
        89 bp
        41.9
        SAMEA2152065_qc_fHP_1
        3.8%
        42%
        72 bp
        16.9
        SAMEA2152065_qc_fHP_2
        3.7%
        41%
        74 bp
        16.9
        SAMEA2152125_qc_fHP_1
        9.9%
        39%
        74 bp
        17.3
        SAMEA2152125_qc_fHP_2
        9.9%
        39%
        74 bp
        17.3
        SAMEA2152204_qc_fHP_1
        19.1%
        41%
        74 bp
        22.1
        SAMEA2152204_qc_fHP_2
        18.6%
        41%
        74 bp
        22.1
        SAMEA2152373_qc_fHP_1
        11.8%
        48%
        89 bp
        32.9
        SAMEA2152373_qc_fHP_2
        11.4%
        48%
        89 bp
        32.9
        SAMEA2152443_qc_fHP_1
        12.4%
        46%
        89 bp
        37.7
        SAMEA2152443_qc_fHP_2
        11.5%
        46%
        89 bp
        37.7
        SAMEA2152521_qc_fHP_1
        9.6%
        44%
        89 bp
        33.9
        SAMEA2152521_qc_fHP_2
        9.4%
        44%
        89 bp
        33.9
        SAMEA2152531_qc_fHP_1
        13.1%
        44%
        89 bp
        36.1
        SAMEA2152531_qc_fHP_2
        12.6%
        44%
        89 bp
        36.1
        SAMEA2152591_qc_fHP_1
        20.0%
        44%
        89 bp
        46.5
        SAMEA2152591_qc_fHP_2
        19.3%
        44%
        89 bp
        46.5
        SAMEA2152938_qc_fHP_1
        9.6%
        47%
        89 bp
        27.5
        SAMEA2152938_qc_fHP_2
        9.5%
        47%
        89 bp
        27.5
        SAMEA2153005_qc_fHP_1
        30.5%
        46%
        89 bp
        33.8
        SAMEA2153005_qc_fHP_2
        29.9%
        46%
        89 bp
        33.8
        SAMEA2153010_qc_fHP_1
        13.0%
        42%
        72 bp
        20.3
        SAMEA2153010_qc_fHP_2
        12.6%
        41%
        74 bp
        20.3
        SAMEA2153251_qc_fHP_1
        18.5%
        44%
        89 bp
        34.8
        SAMEA2153251_qc_fHP_2
        17.9%
        44%
        89 bp
        34.8
        SAMEA2153397_qc_fHP_1
        12.3%
        44%
        89 bp
        37.6
        SAMEA2153397_qc_fHP_2
        11.9%
        44%
        89 bp
        37.6
        SAMEA2153557_qc_fHP_1
        18.8%
        41%
        72 bp
        20.5
        SAMEA2153557_qc_fHP_2
        18.9%
        41%
        74 bp
        20.5
        SAMEA2153852_qc_fHP_1
        9.7%
        46%
        89 bp
        44.5
        SAMEA2153852_qc_fHP_2
        9.5%
        46%
        89 bp
        44.5
        SAMEA2153898_qc_fHP_1
        54.2%
        48%
        89 bp
        44.5
        SAMEA2153898_qc_fHP_2
        52.9%
        48%
        89 bp
        44.5
        SAMEA2154015_qc_fHP_1
        10.6%
        46%
        89 bp
        39.0
        SAMEA2154015_qc_fHP_2
        10.3%
        46%
        89 bp
        39.0
        SAMEA2154036_qc_fHP_1
        17.2%
        43%
        89 bp
        35.3
        SAMEA2154036_qc_fHP_2
        16.7%
        43%
        89 bp
        35.3
        SAMEA2154047_qc_fHP_1
        8.1%
        39%
        74 bp
        15.0
        SAMEA2154047_qc_fHP_2
        9.1%
        39%
        74 bp
        15.0
        SAMEA2154150_qc_fHP_1
        19.4%
        43%
        89 bp
        39.3
        SAMEA2154150_qc_fHP_2
        18.9%
        43%
        89 bp
        39.3
        SAMEA2154452_qc_fHP_1
        7.2%
        40%
        72 bp
        16.0
        SAMEA2154452_qc_fHP_2
        6.9%
        40%
        74 bp
        16.0
        SAMEA2154516_qc_fHP_1
        33.7%
        44%
        89 bp
        27.0
        SAMEA2154516_qc_fHP_2
        33.6%
        44%
        89 bp
        27.0
        SAMEA2154561_qc_fHP_1
        12.9%
        45%
        89 bp
        36.0
        SAMEA2154561_qc_fHP_2
        12.4%
        45%
        89 bp
        36.0
        SAMEA2154620_qc_fHP_1
        6.9%
        46%
        89 bp
        36.2
        SAMEA2154620_qc_fHP_2
        6.9%
        46%
        89 bp
        36.2
        SAMEA2154893_qc_fHP_1
        14.7%
        41%
        68 bp
        16.0
        SAMEA2154893_qc_fHP_2
        14.4%
        41%
        74 bp
        16.0
        SAMEA2154920_qc_fHP_1
        19.4%
        41%
        68 bp
        16.8
        SAMEA2154920_qc_fHP_2
        19.0%
        41%
        74 bp
        16.8
        SAMEA2154992_qc_fHP_1
        7.6%
        40%
        72 bp
        18.8
        SAMEA2154992_qc_fHP_2
        7.4%
        40%
        74 bp
        18.8
        SAMEA2155093_qc_fHP_1
        30.6%
        46%
        89 bp
        34.4
        SAMEA2155093_qc_fHP_2
        30.0%
        46%
        89 bp
        34.4
        SAMEA2155134_qc_fHP_1
        9.0%
        44%
        89 bp
        39.2
        SAMEA2155134_qc_fHP_2
        8.7%
        44%
        89 bp
        39.2
        SAMEA2155255_qc_fHP_1
        7.4%
        47%
        89 bp
        37.1
        SAMEA2155255_qc_fHP_2
        7.2%
        47%
        89 bp
        37.1
        SAMEA2155310_qc_fHP_1
        8.8%
        40%
        72 bp
        19.9
        SAMEA2155310_qc_fHP_2
        8.6%
        40%
        74 bp
        19.9
        SAMEA2155373_qc_fHP_1
        8.6%
        41%
        72 bp
        19.1
        SAMEA2155373_qc_fHP_2
        8.3%
        41%
        74 bp
        19.1
        SAMEA2155512_qc_fHP_1
        18.8%
        45%
        89 bp
        41.3
        SAMEA2155512_qc_fHP_2
        18.3%
        45%
        89 bp
        41.3
        SAMEA2155520_qc_fHP_1
        13.3%
        44%
        89 bp
        33.5
        SAMEA2155520_qc_fHP_2
        12.5%
        44%
        89 bp
        33.5
        SAMEA2155636_qc_fHP_1
        6.8%
        43%
        72 bp
        17.6
        SAMEA2155636_qc_fHP_2
        6.6%
        43%
        74 bp
        17.6
        SAMEA2155689_qc_fHP_1
        11.8%
        40%
        74 bp
        15.9
        SAMEA2155689_qc_fHP_2
        10.5%
        40%
        74 bp
        15.9
        SAMEA2155758_qc_fHP_1
        8.7%
        47%
        89 bp
        34.8
        SAMEA2155758_qc_fHP_2
        8.4%
        47%
        89 bp
        34.8
        SAMEA2155902_qc_fHP_1
        19.2%
        46%
        89 bp
        34.9
        SAMEA2155902_qc_fHP_2
        18.8%
        46%
        89 bp
        34.9
        SAMEA2156032_qc_fHP_1
        29.2%
        46%
        89 bp
        36.1
        SAMEA2156032_qc_fHP_2
        28.4%
        46%
        89 bp
        36.1
        SAMEA2156362_qc_fHP_1
        11.0%
        41%
        72 bp
        16.4
        SAMEA2156362_qc_fHP_2
        9.9%
        41%
        74 bp
        16.4
        SAMEA2156486_qc_fHP_1
        7.3%
        45%
        89 bp
        38.9
        SAMEA2156486_qc_fHP_2
        7.3%
        45%
        89 bp
        38.9
        SAMEA2156577_qc_fHP_1
        12.3%
        46%
        89 bp
        30.7
        SAMEA2156577_qc_fHP_2
        11.9%
        46%
        89 bp
        30.7
        SAMEA2156675_qc_fHP_1
        11.5%
        44%
        74 bp
        24.4
        SAMEA2156675_qc_fHP_2
        11.4%
        44%
        74 bp
        24.4
        SAMEA2156714_qc_fHP_1
        11.8%
        46%
        89 bp
        35.7
        SAMEA2156714_qc_fHP_2
        11.3%
        46%
        89 bp
        35.7
        SAMEA2156850_qc_fHP_1
        10.2%
        47%
        89 bp
        39.9
        SAMEA2156850_qc_fHP_2
        10.0%
        47%
        89 bp
        39.9
        SAMEA2156906_qc_fHP_1
        16.6%
        44%
        72 bp
        18.6
        SAMEA2156906_qc_fHP_2
        16.8%
        44%
        74 bp
        18.6
        SAMEA2157028_qc_fHP_1
        16.4%
        41%
        74 bp
        31.4
        SAMEA2157028_qc_fHP_2
        16.4%
        41%
        74 bp
        31.4
        SAMEA2157192_qc_fHP_1
        10.4%
        41%
        72 bp
        15.3
        SAMEA2157192_qc_fHP_2
        10.1%
        41%
        74 bp
        15.3
        SAMEA2157273_qc_fHP_1
        11.9%
        39%
        74 bp
        16.6
        SAMEA2157273_qc_fHP_2
        11.5%
        39%
        74 bp
        16.6
        SAMEA2157747_qc_fHP_1
        14.5%
        42%
        74 bp
        25.1
        SAMEA2157747_qc_fHP_2
        14.6%
        42%
        74 bp
        25.1
        SAMEA2157793_qc_fHP_1
        6.3%
        42%
        74 bp
        11.9
        SAMEA2157793_qc_fHP_2
        5.6%
        42%
        74 bp
        11.9
        SAMEA2157850_qc_fHP_1
        14.7%
        45%
        89 bp
        40.3
        SAMEA2157850_qc_fHP_2
        14.5%
        45%
        89 bp
        40.3
        SAMEA2157909_qc_fHP_1
        23.4%
        43%
        72 bp
        19.4
        SAMEA2157909_qc_fHP_2
        23.7%
        43%
        74 bp
        19.4
        SAMEA2157917_qc_fHP_1
        12.9%
        47%
        89 bp
        35.2
        SAMEA2157917_qc_fHP_2
        12.6%
        47%
        89 bp
        35.2
        SAMEA2157972_qc_fHP_1
        8.9%
        46%
        89 bp
        43.9
        SAMEA2157972_qc_fHP_2
        8.7%
        46%
        89 bp
        43.9
        SAMEA2157977_qc_fHP_1
        11.1%
        46%
        89 bp
        27.7
        SAMEA2157977_qc_fHP_2
        10.7%
        46%
        89 bp
        27.7
        SAMEA2158039_qc_fHP_1
        10.5%
        46%
        89 bp
        35.0
        SAMEA2158039_qc_fHP_2
        10.2%
        46%
        89 bp
        35.0
        SAMEA2158062_qc_fHP_1
        10.3%
        47%
        89 bp
        43.3
        SAMEA2158062_qc_fHP_2
        10.2%
        47%
        89 bp
        43.3
        SAMEA2158100_qc_fHP_1
        7.6%
        41%
        72 bp
        18.8
        SAMEA2158100_qc_fHP_2
        7.4%
        41%
        74 bp
        18.8
        SAMEA2158190_qc_fHP_1
        13.8%
        47%
        89 bp
        28.7
        SAMEA2158190_qc_fHP_2
        13.4%
        47%
        89 bp
        28.7
        SAMEA2158269_qc_fHP_1
        17.1%
        42%
        74 bp
        28.1
        SAMEA2158269_qc_fHP_2
        16.7%
        42%
        74 bp
        28.1
        SAMEA2158408_qc_fHP_1
        15.7%
        40%
        72 bp
        18.1
        SAMEA2158408_qc_fHP_2
        14.4%
        40%
        74 bp
        18.1
        SAMEA2158454_qc_fHP_1
        6.9%
        41%
        72 bp
        18.4
        SAMEA2158454_qc_fHP_2
        6.9%
        41%
        74 bp
        18.4
        SAMEA2158468_qc_fHP_1
        8.4%
        46%
        89 bp
        36.8
        SAMEA2158468_qc_fHP_2
        8.1%
        46%
        89 bp
        36.8
        SAMEA2158521_qc_fHP_1
        6.5%
        42%
        72 bp
        15.9
        SAMEA2158521_qc_fHP_2
        6.3%
        42%
        74 bp
        15.9
        SAMEA2158542_qc_fHP_1
        8.4%
        47%
        89 bp
        36.1
        SAMEA2158542_qc_fHP_2
        8.0%
        47%
        89 bp
        36.1
        SAMEA2158769_qc_fHP_1
        10.2%
        46%
        89 bp
        33.5
        SAMEA2158769_qc_fHP_2
        9.8%
        46%
        89 bp
        33.5
        SAMEA2159032_qc_fHP_1
        11.2%
        45%
        89 bp
        37.5
        SAMEA2159032_qc_fHP_2
        10.7%
        45%
        89 bp
        37.5
        SAMEA2159102_qc_fHP_1
        11.1%
        46%
        89 bp
        24.8
        SAMEA2159102_qc_fHP_2
        11.0%
        46%
        89 bp
        24.8
        SAMEA2159162_qc_fHP_1
        13.9%
        44%
        89 bp
        37.3
        SAMEA2159162_qc_fHP_2
        13.4%
        45%
        89 bp
        37.3
        SAMEA2159202_qc_fHP_1
        17.9%
        46%
        89 bp
        26.7
        SAMEA2159202_qc_fHP_2
        17.4%
        46%
        89 bp
        26.7
        SAMEA2159338_qc_fHP_1
        7.9%
        46%
        89 bp
        26.7
        SAMEA2159338_qc_fHP_2
        7.7%
        46%
        89 bp
        26.7
        SAMEA2159408_qc_fHP_1
        13.8%
        39%
        74 bp
        27.8
        SAMEA2159408_qc_fHP_2
        13.5%
        39%
        74 bp
        27.8
        SAMEA2159429_qc_fHP_1
        11.7%
        41%
        72 bp
        22.0
        SAMEA2159429_qc_fHP_2
        11.5%
        41%
        74 bp
        22.0
        SAMEA2159529_qc_fHP_1
        14.3%
        45%
        89 bp
        35.2
        SAMEA2159529_qc_fHP_2
        14.0%
        45%
        89 bp
        35.2
        SAMEA2159561_qc_fHP_1
        23.5%
        41%
        74 bp
        17.9
        SAMEA2159561_qc_fHP_2
        23.0%
        40%
        74 bp
        17.9
        SAMEA2159881_qc_fHP_1
        10.2%
        48%
        89 bp
        34.1
        SAMEA2159881_qc_fHP_2
        10.0%
        48%
        89 bp
        34.1
        SAMEA2159891_qc_fHP_1
        6.1%
        40%
        74 bp
        13.5
        SAMEA2159891_qc_fHP_2
        4.4%
        39%
        74 bp
        13.5
        SAMEA2159974_qc_fHP_1
        10.2%
        46%
        89 bp
        29.0
        SAMEA2159974_qc_fHP_2
        10.1%
        46%
        89 bp
        29.0
        SAMEA2160045_qc_fHP_1
        5.9%
        41%
        72 bp
        17.4
        SAMEA2160045_qc_fHP_2
        5.6%
        41%
        74 bp
        17.4
        SAMEA2160152_qc_fHP_1
        25.9%
        45%
        89 bp
        42.5
        SAMEA2160152_qc_fHP_2
        25.0%
        45%
        89 bp
        42.5
        SAMEA2160437_qc_fHP_1
        5.1%
        41%
        72 bp
        14.8
        SAMEA2160437_qc_fHP_2
        4.9%
        41%
        74 bp
        14.8
        SAMEA2160490_qc_fHP_1
        10.5%
        46%
        89 bp
        35.6
        SAMEA2160490_qc_fHP_2
        10.1%
        46%
        89 bp
        35.6
        SAMEA2160616_qc_fHP_1
        6.3%
        47%
        89 bp
        30.9
        SAMEA2160616_qc_fHP_2
        6.1%
        47%
        89 bp
        30.9
        SAMEA2160902_qc_fHP_1
        30.0%
        44%
        89 bp
        31.5
        SAMEA2160902_qc_fHP_2
        29.1%
        44%
        89 bp
        31.5
        SAMEA2160998_qc_fHP_1
        10.7%
        46%
        89 bp
        37.0
        SAMEA2160998_qc_fHP_2
        10.3%
        46%
        89 bp
        37.0
        SAMEA2161021_qc_fHP_1
        20.4%
        35%
        74 bp
        18.0
        SAMEA2161021_qc_fHP_2
        19.6%
        34%
        74 bp
        18.0
        SAMEA2161222_qc_fHP_1
        14.4%
        41%
        74 bp
        26.5
        SAMEA2161222_qc_fHP_2
        14.3%
        41%
        74 bp
        26.5
        SAMEA2161311_qc_fHP_1
        15.3%
        45%
        89 bp
        40.4
        SAMEA2161311_qc_fHP_2
        14.3%
        45%
        89 bp
        40.4
        SAMEA2161372_qc_fHP_1
        17.3%
        43%
        89 bp
        45.6
        SAMEA2161372_qc_fHP_2
        17.0%
        43%
        89 bp
        45.6
        SAMEA2161597_qc_fHP_1
        11.2%
        49%
        89 bp
        35.9
        SAMEA2161597_qc_fHP_2
        10.7%
        49%
        89 bp
        35.9
        SAMEA2161657_qc_fHP_1
        14.0%
        44%
        89 bp
        29.9
        SAMEA2161657_qc_fHP_2
        13.6%
        44%
        89 bp
        29.9
        SAMEA2161897_qc_fHP_1
        32.5%
        44%
        89 bp
        52.3
        SAMEA2161897_qc_fHP_2
        32.0%
        44%
        89 bp
        52.3
        SAMEA2162036_qc_fHP_1
        7.4%
        45%
        89 bp
        35.9
        SAMEA2162036_qc_fHP_2
        7.2%
        45%
        89 bp
        35.9
        SAMEA2162182_qc_fHP_1
        8.5%
        43%
        74 bp
        26.6
        SAMEA2162182_qc_fHP_2
        8.5%
        42%
        74 bp
        26.6
        SAMEA2162200_qc_fHP_1
        9.4%
        41%
        72 bp
        16.6
        SAMEA2162200_qc_fHP_2
        9.3%
        41%
        74 bp
        16.6
        SAMEA2162231_qc_fHP_1
        16.5%
        40%
        74 bp
        25.3
        SAMEA2162231_qc_fHP_2
        16.1%
        40%
        74 bp
        25.3
        SAMEA2162259_qc_fHP_1
        10.5%
        42%
        72 bp
        16.8
        SAMEA2162259_qc_fHP_2
        10.1%
        42%
        74 bp
        16.8
        SAMEA2162475_qc_fHP_1
        16.8%
        44%
        89 bp
        38.7
        SAMEA2162475_qc_fHP_2
        16.5%
        45%
        89 bp
        38.7
        SAMEA2162573_qc_fHP_1
        37.2%
        45%
        89 bp
        37.7
        SAMEA2162573_qc_fHP_2
        36.0%
        46%
        89 bp
        37.7
        SAMEA2162640_qc_fHP_1
        15.5%
        44%
        89 bp
        41.2
        SAMEA2162640_qc_fHP_2
        15.3%
        45%
        89 bp
        41.2
        SAMEA2162811_qc_fHP_1
        13.9%
        46%
        89 bp
        41.4
        SAMEA2162811_qc_fHP_2
        13.5%
        46%
        89 bp
        41.4
        SAMEA2162844_qc_fHP_1
        14.5%
        44%
        89 bp
        39.0
        SAMEA2162844_qc_fHP_2
        14.3%
        44%
        89 bp
        39.0
        SAMEA2162862_qc_fHP_1
        8.0%
        41%
        74 bp
        15.7
        SAMEA2162862_qc_fHP_2
        7.8%
        41%
        74 bp
        15.7
        SAMEA2162880_qc_fHP_1
        27.0%
        39%
        72 bp
        17.3
        SAMEA2162880_qc_fHP_2
        24.8%
        39%
        74 bp
        17.3
        SAMEA2163248_qc_fHP_1
        5.3%
        40%
        72 bp
        15.6
        SAMEA2163248_qc_fHP_2
        5.1%
        40%
        74 bp
        15.6
        SAMEA2163351_qc_fHP_1
        17.2%
        41%
        72 bp
        18.4
        SAMEA2163351_qc_fHP_2
        15.7%
        41%
        74 bp
        18.4
        SAMEA2163432_qc_fHP_1
        11.7%
        47%
        89 bp
        44.3
        SAMEA2163432_qc_fHP_2
        11.6%
        47%
        89 bp
        44.3
        SAMEA2163504_qc_fHP_1
        10.5%
        42%
        72 bp
        15.3
        SAMEA2163504_qc_fHP_2
        10.3%
        42%
        74 bp
        15.3
        SAMEA2163575_qc_fHP_1
        9.7%
        40%
        74 bp
        26.4
        SAMEA2163575_qc_fHP_2
        9.5%
        40%
        74 bp
        26.4
        SAMEA2163583_qc_fHP_1
        9.6%
        46%
        89 bp
        37.9
        SAMEA2163583_qc_fHP_2
        9.4%
        46%
        89 bp
        37.9

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

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        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

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        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

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        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

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        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

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        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

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        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

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        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        414 samples had less than 1% of reads made up of overrepresented sequences

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        No samples found with any adapter contamination > 0.1%

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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        MultiQC v1.14 - Written by Phil Ewels, available on GitHub.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.